AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifnr_hpyl_opreg_100.orf -g0.389 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0144 300 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN) #2 HP0376 55 ferrochelatase (hemH) #3 HP0377 76 thiol:disulfide interchange protein (dsbC), putative #4 HP0723 128 L-asparaginase II (ansB) #5 HP0730 91 H. pylori predicted coding region HP0730 #6 HP0733 119 H. pylori predicted coding region HP0733 Motif number 1 AACGCTTGGCTTTATTTTTGTATTTTCATG 1 25 0 TTTATTTTTG 0.917071 -276 GCAACGCTGTTGTATTTTTTAGGCGCACCG 1 70 0 TGTATTTTTT 0.883611 -231 AGCTTAATTTTTAATCTTTTTCTGTAACAT 1 213 0 TTAATCTTTT 0.979877 -88 AGATTAAAAATTAAGCTTTTTGAAAAAGAT 1 226 1 TTAAGCTTTT 0.938937 -75 ATTATAAAATTTTATCTTTTTCAAAAAGCT 1 239 0 TTTATCTTTT 0.987048 -62 TATAATTATGTTTATCTTTGTTGAATTTAC 1 263 1 TTTATCTTTG 0.974665 -38 TTTCTAACGATTTATTTTTTATTAATCGTT 2 18 1 TTTATTTTTT 0.956343 -38 TTATTTTTTATTAATCGTTTTATTTTAGCA 2 29 1 TTAATCGTTT 0.938967 -27 GTAATAACCTTTATCTTTTAATAGATTTG 3 58 0 TTTATCTTTT 0.987048 -19 TTGAAATTGTTGATTCTTTTATTTTGTTTG 4 97 1 TGATTCTTTT 0.775128 -32 TAGCAAGCGTTTTAGCGTTGGCGCATTCGG 5 26 0 TTTAGCGTTG 0.793385 -66 AGCGGTGTTTTAAATCTTTTAAAGGAAAGG 5 70 1 TAAATCTTTT 0.860843 -22 GGGGTTTGCGTTTTTTTTTTTTTGTTAAAA 6 70 1 TTTTTTTTTT 0.817322 -50 ********** Masking position 8 Map Score: 21.4593 Number of sites scoring better than the average of aligned sites = 1034 Number in coding regions = 820 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 CCTATAATCATGCCCATGAAAATACAAAAAT 1 5 1 TACATGGAAA 0.989349 -296 GGCTAAAGGTTAAACATGATTAAACAAACCCTCATCA 1 120 0 TACATGACAA 0.916481 -181 CAATTTGGCTTAAAAATGCCATTCAAATGGGATTGAG 1 168 1 TAAATGCAAA 0.940437 -133 GATTGAGTTATTACAATGTTACAGAAAAAGATTAAAA 1 198 1 TAAATGGAAA 0.985535 -103 TCAACAAAGATAAACATAATTATAAAATTTTATCTTT 1 250 0 TACATAAAAA 0.968391 -51 AACCTTTATCTTTTAATAGATTTGAAAACTAGGTATC 3 45 0 TTAATAGAAA 0.846769 -32 TAAAACATCGTTAAAATAAATTTAAAAAGGGTTA 4 8 0 TAAATAAAAA 0.958025 -121 TGGTCCATAATGAGAATATTTTTGAAATTGTTGATTC 4 76 1 TAAATAGAAA 0.973237 -53 AAGTTAGCCATAAGGCTAAAAGCACGGCTAA 6 5 1 TGCATAAAAA 0.929443 -115 TTTTTTTTTGTTAAAATGCGTCAGAAAATTCGGCATG 6 84 1 TAAATGGAAA 0.985764 -36 GTCAGAAAATTCGGCATGAGGGCAAAA 6 103 1 TGCATGAAAA 0.96162 -17 * * **** **** Masking position 6 Map Score: 12.7028 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 181 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 ACAAAAATAAAGCCAAGCGTTAGGTCTTAAC 1 34 1 AGCCAGCGTT 0.962736 -267 AAAATACAACAGCGTTGCGATAAAAAAAGGG 1 82 1 AGCGTGCGAT 0.75713 -219 TCATCATTCTTGCCCCTTTTTTTATCGCAAC 1 95 0 TGCCCTTTTT 0.891281 -206 TGTAGTAAGATACCTAGTTTTCAAATCTATT 3 37 1 TACCAGTTTT 0.822892 -40 AATTTATTTTAACGATGTTTTACTATACTAT 4 23 1 AACGTGTTTT 0.880207 -106 TTGGCTAGTAAGCGGTGTTTTAAATCTTTTA 5 60 1 AGCGTGTTTT 0.979515 -32 GCCACGCTTTAGCCGTGCTTTTAGCCTTATG 6 19 0 AGCCTGCTTT 0.991 -101 GCCACGCTTTAGCCACGCTTTAGCCGTGCTT 6 30 0 AGCCCGCTTT 0.99082 -90 CCCACGCTCCAGCCACGCTTTAGCCACGCTT 6 41 0 AGCCCGCTTT 0.99082 -79 CGTGGGGGTTTGCGTTTTTTTTTTTTTGTTA 6 66 1 TGCGTTTTTT 0.829759 -54 TTTGCCCTCATGCCGAATTTTCTGACGCATT 6 98 0 TGCCAATTTT 0.747259 -22 **** ****** Masking position 11 Map Score: 11.2602 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 756 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TTGGCTTTATTTTTGTATTTTCATGGGCAT 1 20 0 TTTTGTATTT 0.925717 -281 ATCGCAACGCTGTTGTATTTTTTAGGCGCA 1 73 0 TGTTGTATTT 0.931041 -228 AAAGATAAAATTTTATAATTATGTTTATCT 1 250 1 TTTTATAATT 0.886499 -51 TGTTTATCTTTGTTGAATTTACTACAAATA 1 271 1 TGTTGAATTT 0.967551 -30 TAACCCTTTTTAAATTTATTTTAACGA 4 8 1 TTTTAAATTT 0.94523 -121 ATGGACCACCTTTTGAAATTAAAAGATTTT 4 54 0 TTTTGAAATT 0.964939 -75 ATGAGAATATTTTTGAAATTGTTGATTCTT 4 85 1 TTTTGAAATT 0.964939 -44 ATTTGTGTTAAAATACCGAATGCGC 5 6 1 TGTTAAAATA 0.746129 -86 GTAAGCGGTGTTTTAAATCTTTTAAAGGAA 5 67 1 TTTTAAATCT 0.782568 -25 TTTTTTTTTTTGTTAAAATGCGTCAGAAAA 6 82 1 TGTTAAAATG 0.813715 -38 ********** Masking position 4 Map Score: 11.7271 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 400 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 ACAAAAATAAAGCCAAGCGTTAGGTCTTAA 1 34 1 AGCCAAGCGT 0.941292 -267 GGGTTTGTTTAATCATGTTTAACCTTTAGC 1 126 1 AATCATGTTT 0.703927 -175 AATTTATTTTAACGATGTTTTACTATACTA 4 23 1 AACGATGTTT 0.903742 -106 TTGGCTAGTAAGCGGTGTTTTAAATCTTTT 5 60 1 AGCGGTGTTT 0.959248 -32 GCCACGCTTTAGCCGTGCTTTTAGCCTTAT 6 20 0 AGCCGTGCTT 0.988794 -100 GCCACGCTTTAGCCACGCTTTAGCCGTGCT 6 31 0 AGCCACGCTT 0.990888 -89 CCCACGCTCCAGCCACGCTTTAGCCACGCT 6 42 0 AGCCACGCTT 0.990888 -78 ********** Masking position 1 Map Score: 6.41773 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 294 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.40931e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0